i dont see why thats a problem? isnt that basically what the xbox1 was and that was a powerhouse of a console compared to its peers (ps2 and gamecube). also one of the biggest knocks against sony during the ps2/ps3 era was the difficulty in programming for the cell and emotion engine... using an x86 based cpu should allow for easier development and porting.
edit: also, developers have chimed in that the orbis dev kit allows for lower level APIs than what directx allows on windows, so even if the hardware is similar to a desktop computer, the ps4 is rumored to have superior efficiency in code:
http://www.neogaf.com/forum/showthread.php?t=512488
http://www.neogaf.com/forum/showthread.php?t=510076